Training – compgenomics

The Biodiversity & Conservation Genomics (BCG) Training Program in the Institute for Systems Genomics (ISG) prepares students to understand how to address conservation challenges using genomic tools. Through a cohort-based model, trainees work on various aspects of the pipeline, from field sampling and experimental design, to sequencing, genome assembly/annotation, and population/landscape genomics. All aspects of the project are connected to agencies invested in applying genomic tools to conservation or biodiversity related challenges.

The program combines training sessions (R/Python, reproducible workflows, open data, data viz), project-based mentorship with ISG/CBC faculty, and hands-on use of UConn’s high-performance computing resources. Trainees engage with agency and NGO partners, contribute to open datasets and tools, and communicate results via posters, talks, and manuscripts. This program is open to undergraduate students from the life sciences, computer/data science, and related fields, BCG emphasizes collaboration, inclusivity, and open science, to prepare students for a career in conservation genomics. Learn more here.

Featured organisms

Publications

Guzman-Torres, C.R., Trybulec, E., LeVasseur, H., Akella, H., Amee, M., Strickland, E., Pauloski, N., Williams, M., Romero-Severson, J., Hoban, S., Wegrzyn, J.L., and Woeste, K. (2024). Conserving a threatened North American walnut: A chromosome-scale reference genome for butternut (Juglans cinerea). G3: Genes, Genomes, Genetics, 14(1): jkad189. https://doi.org/10.1093/g3journal/jkad189

Funding

The NSF-funded Research and Mentoring for Postbaccalaureates (RaMP) Program at UConn provides a year-long, immersive research experience for recent college graduates, with an emphasis on broadening participation in STEM. Anchored in the theme of genomic novelty, the program explores how genomes evolve, what drives the novel genomic features, and how these innovations shape phenotype and adaptation. RaMP scholars join independent labs and also participate in a cohort project where they receive structured training that integrates wet-lab skills, computational biology, and professional development.

After the initial “bridge to research” period focused on core skills in sequencing, bioinformatics, and experimental design, the full cohort works collaboratively on generating a new genomic resource for a species lacking foundational data. Past cohorts have produced chromosome-scale genome assemblies for organisms such as scorpions and subspecies of Everglades mink. Each cohort publishes a shared first-author manuscript at the end of the project. Learn more here.

Featured organisms

Publications

Affini, A., Baranowski, H., Forbes, S., Foust, E. N., Hatley, K., Ni, E. L., McGuire, A., Paist, K., Rutter, M., Smith, R. N., Vargas, N., Akella, H., Castellano, K., Pauloski, N., Reid, N., O’Neill, R., King, T., Jockusch, E. L., Wegrzyn, J. L., & Hapeman, P. (2025). Mink by mink: stitching together signatures of subspecies adaptation through a pangenome of threatened mustelids. bioRxiv, 2025.07.25.666817. https://www.biorxiv.org/content/10.1101/2025.07.25.666817v1.abstract

Bryant, M.J., Coello, A.M., Glendening, A.M., Hilliman, S.A., Jara, C.F., Pring, S.S., Rodríguez Rivera, A., Santiago Membreño, J., Nigro, L., Pauloski, N., Graham, M.R., King, T., Jockusch, E.L., O’Neill, R.J., Wegrzyn, J.L., Santibáñez-López, C.E., and Webster, C.N. (2024). Unveiling the genetic blueprint of a desert scorpion: A chromosome-level genome of Hadrurus arizonensis provides the first reference for Parvorder Iurida. Genome Biology and Evolution, 16(5): evae097. https://doi.org/10.1093/gbe/evae097

Featured organisms

Publications

Funding

Research and Mentoring for Postbaccalaureates (RAMP)

Featured organisms

Publications

Funding

U.S National Science Foundation

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